SRI VENKATESWARA COLLEGE OF ENGINEERING

SVCE INNOVATES 2019

STUDENTS’ RESEARCH DAY

Registration form

Title of the Innovative idea/Project:

Analyzing and implementation of algorithms in computational molecular biology.

Details of the team

Team Name Branch Mail Id Mobile number

Member & Year
1 NILESH D I – IT nileshlund@gmail.com 9670 57592

2 SANTHOSH P I - BT 93846 60198

Faculty NIVETHAA SHREE K nivethaashree@svce.ac.in

(Mentor)

Broad areas under which this research work can be categorized:

1. Design And Analysis Of Algorithms

2. Computational Molecular Biology

SVCE INNOVATES 2019

Team ID (to be assigned by department coordinator): 180801069

ABSTRACT

Researchers: Nilesh D, Santhosh P

Presentation Title: Analyzing and implementation of algorithms in computational

molecular biology
Research Focus: Bioinformatics
College: Sri Venkateswara College Of Engineering (SVCE)
Presentation Type: Software-aided
Computational biology involves the development and application of data-analytical and
theoretical methods, mathematical modelling and computational simulation techniques to
the study of biological, ecological, behavioural, and social systems. The field is broadly
defined and includes foundations in molecular biology, applied mathematics, computer
science and evolution.
A staple in any accredited undergraduate curriculum in Computer Science is a course in
'The Design and Analysis of Algorithms'. This project provides some specific algorithms
and problems from bioinformatics that can be used to illustrate a variety of design
techniques in an algorithms course. The project then discusses the major algorithm design
techniques including brute force, dynamic programming, and graph problems. For each
of these design techniques, the bioinformatics problem of nucleotide and protein
sequence alignment is discussed and solved.

The following algorithms were implemented, analysed and studied:-

1. DNA Sequencing – A Brute-Force Approach

A single DNA sequence was stored in a file and the following were determined:-
 Length of the DNA sequence
 Percentage of GC Content present in the DNA sequence
 The reversed DNA sequence

2. Longest Common Subsequence

This algorithm, printing the Longest Common Subsequence problem falls under
Dynamic programming and has been implemented two compare two DNA strands
and get the lengthiest subsequence of all the generated subsequences and print its
length. It also focuses on avoiding the overlapping i.e., avoid calculating the
subsequence that has already been generated.

3. Euler’s Graph

Find a cycle that visits every cycle once in linear time. This algorithm abandons
the classical “overlap–layout–consensus” approach in favour of a new Euler
algorithm that, for the first time, resolves the 20-year-old “repeat problem” in
fragment assembly. Our main result is the reduction of the fragment assembly to a
variation of the classical Eulerian path problem that allows one to generate
accurate solutions of large-scale sequencing problems.

The motivation for this project stems from a desire to spice up the traditional
'Design and Analysis of Algorithms' subject by studying concepts from the
exciting and rapidly expanding field of bioinformatics.